rs334543

Variant names:

• chr3-120113774-C-A
• rs334543
• ENST00000484076.1:n.415+8929C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-120113774-C-A
• chr3-120113774-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484076.1(GSK3B-DT):​n.415+8929C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,046 control chromosomes in the GnomAD database, including 42,069 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42069 hom., cov: 31)
• Consequence: GSK3B-DT ENST00000484076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 16 publications found

Genes affected

GSK3B-DT (HGNC:55635): (GSK3B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.415+8929C>A		intron	N/A
	GSK3B-DT	ENST00000834988.1		n.309+14795C>A		intron	N/A
	GSK3B-DT	ENST00000834989.1		n.482+17996C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112155 AN: 151928 Hom.: 42021 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.713

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.738 AC: 112247 AN: 152046 Hom.: 42069 Cov.: 31 AF XY: 0.736 AC XY: 54678 AN XY: 74316

African (AFR) AF: 0.873 AC: 36209 AN: 41490

American (AMR) AF: 0.614 AC: 9386 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2397 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3466 AN: 5140

South Asian (SAS) AF: 0.811 AC: 3909 AN: 4822

European-Finnish (FIN) AF: 0.694 AC: 7323 AN: 10550

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47300 AN: 67976

Other (OTH) AF: 0.714 AC: 1505 AN: 2108

Alfa AF: 0.701 Hom.: 69548

Bravo AF: 0.732

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.1
DANN	Benign	0.82
PhyloP100		-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs334543;

hg19: chr3-119832621;